The Atlantic salmon genome provides insights into rediploidization
Abstract The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we pres...
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Springer Science and Business Media LLC
2016
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crspringernat:10.1038/nature17164 2023-05-15T15:30:22+02:00 The Atlantic salmon genome provides insights into rediploidization Lien, Sigbjørn Koop, Ben F. Sandve, Simen R. Miller, Jason R. Kent, Matthew P. Nome, Torfinn Hvidsten, Torgeir R. Leong, Jong S. Minkley, David R. Zimin, Aleksey Grammes, Fabian Grove, Harald Gjuvsland, Arne Walenz, Brian Hermansen, Russell A. von Schalburg, Kris Rondeau, Eric B. Di Genova, Alex Samy, Jeevan K. A. Olav Vik, Jon Vigeland, Magnus D. Caler, Lis Grimholt, Unni Jentoft, Sissel Inge Våge, Dag de Jong, Pieter Moen, Thomas Baranski, Matthew Palti, Yniv Smith, Douglas R. Yorke, James A. Nederbragt, Alexander J. Tooming-Klunderud, Ave Jakobsen, Kjetill S. Jiang, Xuanting Fan, Dingding Hu, Yan Liberles, David A. Vidal, Rodrigo Iturra, Patricia Jones, Steven J. M. Jonassen, Inge Maass, Alejandro Omholt, Stig W. Davidson, William S. 2016 http://dx.doi.org/10.1038/nature17164 http://www.nature.com/articles/nature17164.pdf http://www.nature.com/articles/nature17164 en eng Springer Science and Business Media LLC https://creativecommons.org/licenses/by/4.0 https://creativecommons.org/licenses/by/4.0 CC-BY Nature volume 533, issue 7602, page 200-205 ISSN 0028-0836 1476-4687 Multidisciplinary journal-article 2016 crspringernat https://doi.org/10.1038/nature17164 2022-01-04T12:57:22Z Abstract The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon ( Salmo salar ), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes. Article in Journal/Newspaper Atlantic salmon Salmo salar Springer Nature (via Crossref) Nature 533 7602 200 205 |
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Open Polar |
collection |
Springer Nature (via Crossref) |
op_collection_id |
crspringernat |
language |
English |
topic |
Multidisciplinary |
spellingShingle |
Multidisciplinary Lien, Sigbjørn Koop, Ben F. Sandve, Simen R. Miller, Jason R. Kent, Matthew P. Nome, Torfinn Hvidsten, Torgeir R. Leong, Jong S. Minkley, David R. Zimin, Aleksey Grammes, Fabian Grove, Harald Gjuvsland, Arne Walenz, Brian Hermansen, Russell A. von Schalburg, Kris Rondeau, Eric B. Di Genova, Alex Samy, Jeevan K. A. Olav Vik, Jon Vigeland, Magnus D. Caler, Lis Grimholt, Unni Jentoft, Sissel Inge Våge, Dag de Jong, Pieter Moen, Thomas Baranski, Matthew Palti, Yniv Smith, Douglas R. Yorke, James A. Nederbragt, Alexander J. Tooming-Klunderud, Ave Jakobsen, Kjetill S. Jiang, Xuanting Fan, Dingding Hu, Yan Liberles, David A. Vidal, Rodrigo Iturra, Patricia Jones, Steven J. M. Jonassen, Inge Maass, Alejandro Omholt, Stig W. Davidson, William S. The Atlantic salmon genome provides insights into rediploidization |
topic_facet |
Multidisciplinary |
description |
Abstract The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon ( Salmo salar ), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes. |
format |
Article in Journal/Newspaper |
author |
Lien, Sigbjørn Koop, Ben F. Sandve, Simen R. Miller, Jason R. Kent, Matthew P. Nome, Torfinn Hvidsten, Torgeir R. Leong, Jong S. Minkley, David R. Zimin, Aleksey Grammes, Fabian Grove, Harald Gjuvsland, Arne Walenz, Brian Hermansen, Russell A. von Schalburg, Kris Rondeau, Eric B. Di Genova, Alex Samy, Jeevan K. A. Olav Vik, Jon Vigeland, Magnus D. Caler, Lis Grimholt, Unni Jentoft, Sissel Inge Våge, Dag de Jong, Pieter Moen, Thomas Baranski, Matthew Palti, Yniv Smith, Douglas R. Yorke, James A. Nederbragt, Alexander J. Tooming-Klunderud, Ave Jakobsen, Kjetill S. Jiang, Xuanting Fan, Dingding Hu, Yan Liberles, David A. Vidal, Rodrigo Iturra, Patricia Jones, Steven J. M. Jonassen, Inge Maass, Alejandro Omholt, Stig W. Davidson, William S. |
author_facet |
Lien, Sigbjørn Koop, Ben F. Sandve, Simen R. Miller, Jason R. Kent, Matthew P. Nome, Torfinn Hvidsten, Torgeir R. Leong, Jong S. Minkley, David R. Zimin, Aleksey Grammes, Fabian Grove, Harald Gjuvsland, Arne Walenz, Brian Hermansen, Russell A. von Schalburg, Kris Rondeau, Eric B. Di Genova, Alex Samy, Jeevan K. A. Olav Vik, Jon Vigeland, Magnus D. Caler, Lis Grimholt, Unni Jentoft, Sissel Inge Våge, Dag de Jong, Pieter Moen, Thomas Baranski, Matthew Palti, Yniv Smith, Douglas R. Yorke, James A. Nederbragt, Alexander J. Tooming-Klunderud, Ave Jakobsen, Kjetill S. Jiang, Xuanting Fan, Dingding Hu, Yan Liberles, David A. Vidal, Rodrigo Iturra, Patricia Jones, Steven J. M. Jonassen, Inge Maass, Alejandro Omholt, Stig W. Davidson, William S. |
author_sort |
Lien, Sigbjørn |
title |
The Atlantic salmon genome provides insights into rediploidization |
title_short |
The Atlantic salmon genome provides insights into rediploidization |
title_full |
The Atlantic salmon genome provides insights into rediploidization |
title_fullStr |
The Atlantic salmon genome provides insights into rediploidization |
title_full_unstemmed |
The Atlantic salmon genome provides insights into rediploidization |
title_sort |
atlantic salmon genome provides insights into rediploidization |
publisher |
Springer Science and Business Media LLC |
publishDate |
2016 |
url |
http://dx.doi.org/10.1038/nature17164 http://www.nature.com/articles/nature17164.pdf http://www.nature.com/articles/nature17164 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
Nature volume 533, issue 7602, page 200-205 ISSN 0028-0836 1476-4687 |
op_rights |
https://creativecommons.org/licenses/by/4.0 https://creativecommons.org/licenses/by/4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1038/nature17164 |
container_title |
Nature |
container_volume |
533 |
container_issue |
7602 |
container_start_page |
200 |
op_container_end_page |
205 |
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1766360812139577344 |